org.obolibrary.oboformat.model

Class OBODoc

java.lang.Object

org.obolibrary.oboformat.model.OBODoc

public class OBODoc
extends Object

An OBODoc is a container for a header frame and zero or more entity frames.

Constructor Summary

Constructors

Constructor and Description
OBODoc() default constructor.

Method Summary

Modifier and Type	Method and Description
void	addDefaultOntologyHeader(String defaultOnt) Adds the default ontology header.
void	addFrame(Frame f) Adds the frame.
void	addImportedOBODoc(OBODoc doc) Adds the imported obo doc.
void	addInstanceFrame(Frame f) Adds the instance frame.
void	addTermFrame(Frame f) Adds the term frame.
void	addTypedefFrame(Frame f) Adds the typedef frame.
void	check() Check this document for violations, i.e.
void	freezeFrames() Freezing an OBODoc signals that the document has become quiescent, and that the system may optimize data structures for performance or space.
Frame	getHeaderFrame()
static String	getIDSpace(String prefix) Looks up the ID prefix to IRI prefix mapping.
Collection<OBODoc>	getImportedOBODocs()
Frame	getInstanceFrame(String id)
Collection<Frame>	getInstanceFrames()
Frame	getTermFrame(String id)
Frame	getTermFrame(String id, boolean followImport)
Collection<Frame>	getTermFrames()
Frame	getTypedefFrame(String id)
Frame	getTypedefFrame(String id, boolean followImports)
Collection<Frame>	getTypedefFrames()
static boolean	isTreatXrefsAsEquivalent(String prefix)
void	mergeContents(OBODoc extDoc) Merge contents.
void	setHeaderFrame(Frame headerFrame)
void	setImportedOBODocs(Collection<OBODoc> importedOBODocs)
String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

OBODoc

public OBODoc()

default constructor.

Method Detail

getHeaderFrame

public Frame getHeaderFrame()

Returns:

the header frame

setHeaderFrame

public void setHeaderFrame(Frame headerFrame)

Parameters:

headerFrame - the new header frame

getTermFrames

@Nonnull
public Collection<Frame> getTermFrames()

Returns:

the term frames

getTypedefFrames

@Nonnull
public Collection<Frame> getTypedefFrames()

Returns:

the typedef frames

getInstanceFrames

@Nonnull
public Collection<Frame> getInstanceFrames()

Returns:

the instance frames

freezeFrames

public void freezeFrames()

Freezing an OBODoc signals that the document has become quiescent, and that the system may optimize data structures for performance or space.

getTermFrame

@Nullable
public Frame getTermFrame(String id)

Parameters:

id - the id

Returns:

the term frame

getTermFrame

@Nullable
public Frame getTermFrame(String id,
                                    boolean followImport)

Parameters:

id - the id

followImport - the follow import

Returns:

the term frame

getTypedefFrame

@Nullable
public Frame getTypedefFrame(String id)

Parameters:

id - the id

Returns:

the typedef frame

getTypedefFrame

@Nullable
public Frame getTypedefFrame(String id,
                                       boolean followImports)

Parameters:

id - the id

followImports - the follow imports

Returns:

the typedef frame

getInstanceFrame

public Frame getInstanceFrame(String id)

Parameters:

id - the id

Returns:

the instance frame

getImportedOBODocs

public Collection<OBODoc> getImportedOBODocs()

Returns:

the imported obo documents

setImportedOBODocs

public void setImportedOBODocs(Collection<OBODoc> importedOBODocs)

Parameters:

importedOBODocs - the new imported obo documents

addImportedOBODoc

public void addImportedOBODoc(OBODoc doc)

Adds the imported obo doc.

Parameters:

doc - the doc

addFrame

public void addFrame(@Nonnull
                     Frame f)
              throws FrameMergeException

Adds the frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addTermFrame

public void addTermFrame(@Nonnull
                         Frame f)
                  throws FrameMergeException

Adds the term frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addTypedefFrame

public void addTypedefFrame(@Nonnull
                            Frame f)
                     throws FrameMergeException

Adds the typedef frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addInstanceFrame

public void addInstanceFrame(@Nonnull
                             Frame f)
                      throws FrameMergeException

Adds the instance frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

getIDSpace

@Nullable
public static String getIDSpace(@Nonnull
                                          String prefix)

Looks up the ID prefix to IRI prefix mapping. Header-Tag: idspace

Parameters:

prefix - prefix

Returns:

IRI prefix as string

isTreatXrefsAsEquivalent

public static boolean isTreatXrefsAsEquivalent(@Nullable
                                               String prefix)

Parameters:

prefix - the prefix

Returns:

true, if xref values should be treated as equivalent

mergeContents

public void mergeContents(@Nonnull
                          OBODoc extDoc)
                   throws FrameMergeException

Merge contents.

Parameters:

extDoc - the external doc

Throws:

FrameMergeException - the frame merge exception

addDefaultOntologyHeader

public void addDefaultOntologyHeader(String defaultOnt)

Adds the default ontology header.

Parameters:

defaultOnt - the default ont

check

public void check()
           throws FrameStructureException

Check this document for violations, i.e. cardinality constraint violations.

Throws:

FrameStructureException - the frame structure exception

See Also:

for equivalent checks in OWL

toString

@Nonnull
public String toString()

Overrides:

toString in class Object